Package index • ordr

‘ordr’ package

A unified framework for ordination objects and biplot methods using tidy principles

ordr ordr-package: ordr package

Functions, classes, and methods

Introducing and adapting ordination techniques for the ordr workflow

lda_ord() predict(<lda_ord>): Augmented implementation of linear discriminant analysis

lra() print(<lra>) screeplot(<lra>) biplot(<lra>) plot(<lra>): Log-ratio analysis

eigen_ord() svd_ord() cmdscale_ord() cancor_ord(): Wrappers for lossy ordination methods

Data sets

Additional data sets used to illustrate ordination techniques

glass: Glass composition data

qswur_usa: U.S. university rankings

Tidy ordination

The ‘tbl_ord’ class wrapper, with methods for accessing components and for querying and manipulating metadata

recover_rows() recover_cols() get_rows() get_cols() as.matrix(<tbl_ord>) recover_inertia() recover_coord() get_coord() get_inertia() dim(<tbl_ord>): Access factors, coordinates, and metadata from ordination objects

recover_aug_rows() recover_aug_cols() recover_aug_coord() augment_ord(): Augment factors and coordinates of 'tbl_ord' objects

tidy(<tbl_ord>) glance(<tbl_ord>) fortify(<tbl_ord>): Tidiers for 'tbl_ord' objects

annotation: Annotate factors of 'tbl_ord' objects

get_negation() revert_negation() negate_ord() negate_to_first_orthant(): Negation of ordination axes

recover_conference() get_conference() revert_conference() confer_inertia(): Confer inertia to factors of a 'tbl_ord' object

recover_supp_rows() recover_supp_cols(): Supplement 'tbl_ord' objects with new data

as_tbl_ord() make_tbl_ord() is_tbl_ord() is.tbl_ord() valid_tbl_ord() un_tbl_ord(): A unified ordination object class

format(<tbl_ord>) print(<tbl_ord>): Format a tbl_ord for printing

plot(<tbl_ord>) screeplot(<tbl_ord>) biplot(<tbl_ord>): Plot and biplot methods for 'tbl_ord' objects

pull_factor() pull_rows() pull_cols() rename_rows() rename_cols() select_rows() select_cols() mutate_rows() mutate_cols() transmute_rows() transmute_cols() cbind_rows() cbind_cols() left_join_rows() left_join_cols(): dplyr verbs for tbl_ord factors

ordinate(): Fit an ordination model to a data object

Layered grammar for biplots

Functions to generate and annotate biplots from ‘tbl_ord’ objects, following the layered grammar of graphics

coord_rect(): Cartesian coordinates and plotting window with fixed aspect ratios

coord_scaffold(): Convenience coordinate system for scaffolding axes

ggbiplot() ord_aes(): Biplots following the grammar of graphics

stat_rows() stat_cols(): Render plot elements for one matrix of an ordination

stat_referent() ggplot_add(<LayerRef>): Transformations with respect to reference data

stat_bagplot(): Bagplots

stat_center() stat_star(): Compute geometric centers and spreads for ordination factors

stat_chull() stat_peel(): Convex hulls and hull peelings

stat_cone(): Conical hull

stat_depth() stat_depth_filled(): Depth estimates and contours

stat_projection(): Project rows onto columns or vice-versa

stat_rule() minpp() maxpp() minabspp(): Construct limited rules offset from the origin

stat_scale(): Multiply artificial coordinates by a scale factor

stat_spantree(): Calculate a minimum spanning tree among cases or variables

geom_origin() geom_unit_circle(): Marker or unit circle at the origin

geom_axis(): Axes through or offset from the origin

geom_bagplot(): Bagplots

geom_interpolation(): Render interpolation of new rows from columns (or vice-versa)

geom_isoline(): Isolines (contour lines)

geom_lineranges() geom_pointranges(): Intervals depicting ranges, usually about center points

geom_rule(): Rulers through or offset from the origin

geom_text_radiate(): Text radiating outward from the origin

geom_vector(): Vectors from the origin

theme_scaffold() theme_biplot(): Scaffolding theme

draw_key_line() draw_key_crosslines() draw_key_crosspoint(): Biplot key drawing functions

ordr-ggproto CoordRect CoordScaffold GeomAxis GeomBagplot GeomInterpolation GeomPointranges GeomLineranges GeomIsoline GeomOrigin GeomUnitCircle GeomRule GeomTextRadiate GeomVector StatChull StatPeel StatDepth StatDepthFilled StatBagplot StatCenter StatStar StatCone StatRows StatCols StatReferent StatProjection StatRule StatScale StatSpantree StatRowsDensity2d StatColsDensity2d StatRowsDensity2dFilled StatColsDensity2dFilled StatRowsEllipse StatColsEllipse StatRowsBagplot StatColsBagplot StatRowsCenter StatColsCenter StatRowsStar StatColsStar StatRowsChull StatColsChull StatRowsPeel StatColsPeel StatRowsCone StatColsCone StatRowsDepth StatColsDepth StatRowsDepthFilled StatColsDepthFilled StatRowsProjection StatColsProjection StatRowsRule StatColsRule StatRowsScale StatColsScale StatRowsSpantree StatColsSpantree: ggproto classes created and adapted for ordr

geom_rows_point() geom_cols_point() geom_rows_path() geom_cols_path() geom_rows_polygon() geom_cols_polygon() geom_rows_contour() geom_cols_contour() geom_rows_density_2d() geom_cols_density_2d() geom_rows_density_2d_filled() geom_cols_density_2d_filled() geom_rows_text() geom_cols_text() geom_rows_label() geom_cols_label() geom_rows_text_repel() geom_cols_text_repel() geom_rows_label_repel() geom_cols_label_repel() geom_rows_axis() geom_cols_axis() geom_rows_bagplot() geom_cols_bagplot() geom_rows_interpolation() geom_cols_interpolation() geom_rows_lineranges() geom_cols_lineranges() geom_rows_pointranges() geom_cols_pointranges() geom_rows_isoline() geom_cols_isoline() geom_rows_rule() geom_cols_rule() geom_rows_text_radiate() geom_cols_text_radiate() geom_rows_vector() geom_cols_vector(): Convenience geoms for row and column matrix factors

stat_rows_density_2d() stat_cols_density_2d() stat_rows_density_2d_filled() stat_cols_density_2d_filled() stat_rows_ellipse() stat_cols_ellipse() stat_rows_bagplot() stat_cols_bagplot() stat_rows_center() stat_cols_center() stat_rows_star() stat_cols_star() stat_rows_chull() stat_cols_chull() stat_rows_peel() stat_cols_peel() stat_rows_cone() stat_cols_cone() stat_rows_depth() stat_cols_depth() stat_rows_depth_filled() stat_cols_depth_filled() stat_rows_projection() stat_cols_projection() stat_rows_rule() stat_cols_rule() stat_rows_scale() stat_cols_scale() stat_rows_spantree() stat_cols_spantree(): Convenience stats for row and column matrix factors

Class methods

Recovery and augmentation methods for ordination model classes

as_tbl_ord(<cancor_ord>) recover_rows(<cancor_ord>) recover_cols(<cancor_ord>) recover_inertia(<cancor_ord>) recover_coord(<cancor_ord>) recover_conference(<cancor_ord>) recover_supp_rows(<cancor_ord>) recover_supp_cols(<cancor_ord>) recover_aug_rows(<cancor_ord>) recover_aug_cols(<cancor_ord>) recover_aug_coord(<cancor_ord>): Functionality for canonical correlations

as_tbl_ord(<cmds_ord>) recover_rows(<cmds_ord>) recover_cols(<cmds_ord>) recover_inertia(<cmds_ord>) recover_coord(<cmds_ord>) recover_conference(<cmds_ord>) recover_aug_rows(<cmds_ord>) recover_aug_cols(<cmds_ord>) recover_aug_coord(<cmds_ord>): Functionality for classical multidimensional scaling objects

as_tbl_ord(<correspondence>) recover_rows(<correspondence>) recover_cols(<correspondence>) recover_inertia(<correspondence>) recover_conference(<correspondence>) recover_coord(<correspondence>) recover_aug_rows(<correspondence>) recover_aug_cols(<correspondence>) recover_aug_coord(<correspondence>): Functionality for correspondence analysis ('correspondence') objects

as_tbl_ord(<eigen>) recover_rows(<eigen>) recover_cols(<eigen>) recover_inertia(<eigen>) recover_coord(<eigen>) recover_conference(<eigen>) recover_aug_rows(<eigen_ord>) recover_aug_cols(<eigen_ord>) recover_aug_coord(<eigen>) as_tbl_ord(<eigen_ord>) recover_rows(<eigen_ord>) recover_cols(<eigen_ord>) recover_inertia(<eigen_ord>) recover_coord(<eigen_ord>) recover_conference(<eigen_ord>) recover_aug_coord(<eigen_ord>): Functionality for eigen-decompositions

as_tbl_ord(<factanal>) recover_rows(<factanal>) recover_cols(<factanal>) recover_inertia(<factanal>) recover_coord(<factanal>) recover_conference(<factanal>) recover_supp_rows(<factanal>) recover_aug_rows(<factanal>) recover_aug_cols(<factanal>) recover_aug_coord(<factanal>): Functionality for factor analysis ('factanal') objects

as_tbl_ord(<kmeans>) recover_rows(<kmeans>) recover_cols(<kmeans>) recover_coord(<kmeans>) recover_aug_rows(<kmeans>) recover_aug_cols(<kmeans>) recover_aug_coord(<kmeans>): Functionality for k-means clustering ('kmeans') objects

as_tbl_ord(<lda>) as_tbl_ord(<lda_ord>) recover_rows(<lda>) recover_rows(<lda_ord>) recover_cols(<lda>) recover_cols(<lda_ord>) recover_inertia(<lda>) recover_inertia(<lda_ord>) recover_coord(<lda>) recover_coord(<lda_ord>) recover_conference(<lda>) recover_conference(<lda_ord>) recover_aug_rows(<lda>) recover_aug_rows(<lda_ord>) recover_aug_cols(<lda>) recover_aug_cols(<lda_ord>) recover_aug_coord(<lda>) recover_aug_coord(<lda_ord>) recover_supp_rows(<lda>) recover_supp_rows(<lda_ord>): Functionality for linear discriminant analysis ('lda') objects

as_tbl_ord(<lm>) recover_rows(<lm>) recover_cols(<lm>) recover_coord(<lm>) recover_aug_rows(<lm>) recover_aug_cols(<lm>) recover_aug_coord(<lm>) recover_aug_rows(<glm>) recover_rows(<mlm>) recover_cols(<mlm>) recover_coord(<mlm>) recover_aug_rows(<mlm>) recover_aug_cols(<mlm>) recover_aug_coord(<mlm>): Functionality for linear model objects

as_tbl_ord(<lra>) recover_rows(<lra>) recover_cols(<lra>) recover_inertia(<lra>) recover_coord(<lra>) recover_conference(<lra>) recover_aug_rows(<lra>) recover_aug_cols(<lra>) recover_aug_coord(<lra>): Functionality for log-ratio analysis ('lra') objects

as_tbl_ord(<mca>) recover_rows(<mca>) recover_cols(<mca>) recover_inertia(<mca>) recover_conference(<mca>) recover_coord(<mca>) recover_supp_rows(<mca>) recover_aug_rows(<mca>) recover_aug_cols(<mca>) recover_aug_coord(<mca>): Functionality for multiple correspondence analysis ('mca') objects

as_tbl_ord(<prcomp>) recover_rows(<prcomp>) recover_cols(<prcomp>) recover_inertia(<prcomp>) recover_coord(<prcomp>) recover_conference(<prcomp>) recover_aug_rows(<prcomp>) recover_aug_cols(<prcomp>) recover_aug_coord(<prcomp>): Functionality for principal components analysis ('prcomp') objects

as_tbl_ord(<princomp>) recover_rows(<princomp>) recover_cols(<princomp>) recover_inertia(<princomp>) recover_coord(<princomp>) recover_conference(<princomp>) recover_supp_rows(<princomp>) recover_aug_rows(<princomp>) recover_aug_cols(<princomp>) recover_aug_coord(<princomp>): Functionality for principal components analysis ('princomp') objects

as_tbl_ord(<svd_ord>) recover_rows(<svd_ord>) recover_cols(<svd_ord>) recover_inertia(<svd_ord>) recover_coord(<svd_ord>) recover_conference(<svd_ord>) recover_aug_rows(<svd_ord>) recover_aug_cols(<svd_ord>) recover_aug_coord(<svd_ord>): Functionality for singular value decompositions